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ensure conda execution is enabled in configuration #5

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merged 3 commits into from
Jul 8, 2024
Merged

ensure conda execution is enabled in configuration #5

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6b9772e
ensure conda execution is enabled in configuration
cpauvert Jul 5, 2024
ace94bf
add tab to beautify the generated nextflow configuration
cpauvert Jul 5, 2024
58be741
Merge branch 'main' into fix-4-with-conda
cpauvert Jul 8, 2024
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5 changes: 4 additions & 1 deletion {{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def append_config_block(nf_config="nextflow.config", scope=None, **kwargs):
with open(nf_config, "a") as f:
f.write(scope.rstrip() + "{" + "\n")
for k in kwargs:
f.write(f"{k} = {kwargs[k]}\n")
f.write(f"\t{k} = {kwargs[k]}\n")
f.write("}\n")


Expand Down Expand Up @@ -138,6 +138,9 @@ def run_nextflow(

# Use conda
if use_conda:
append_config_block(
scope="conda", enabled='"true"'
)
if conda_frontend == "mamba":
append_config_block(
scope="conda", useMamba='"true"', cacheDir=f'"{conda_prefix}"'
Expand Down
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